By disrupting normal gut microbiota, antibiotic therapies pose a major risk to the treatment of Clostridium difficile infection (CDI), a debilitating and potentially fatal intestinal infection. Consequently, there is a pressing need for the development of an effective, novel, nonantibiotic treatment. One such treatment is fecal microbiota therapy (FMT), which restores gut microbiota in CDI patients and has gained popularity in recent years due to its high efficacy rate. Health Canada has recently proposed to regulate FMT as a “biological drug” following the U.S. Food and Drug Administration’s approach. Moreover, as an interim policy, Health Canada proposed to exercise a risk-based interpretation regarding the clinical trial requirements for FMT used in treating CDI, limited to patients unresponsive to conventional therapies. This article first discusses important considerations for an alternative classification of FMT and stresses the need to develop a policy dependent upon scientific developments in the field, away from a one-size-fits-all approach. Second, it briefly explores some concerns related to the recourse to this provisional interpretation to guide the use of FMT in the treatment of patients with CDI unresponsive to conventional therapies subject to Health Canada’s recent policy.